Incidental Mutation 'R8162:Kdm2b'
ID 633565
Institutional Source Beutler Lab
Gene Symbol Kdm2b
Ensembl Gene ENSMUSG00000029475
Gene Name lysine (K)-specific demethylase 2B
Synonyms Cxxc2, Fbxl10, Jhdm1b
MMRRC Submission 067588-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R8162 (G1)
Quality Score 225.009
Status Validated
Chromosome 5
Chromosomal Location 123008727-123127333 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 123072856 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Asparagine at position 341 (Y341N)
Ref Sequence ENSEMBL: ENSMUSP00000038229 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046073] [ENSMUST00000086200] [ENSMUST00000118027] [ENSMUST00000121739] [ENSMUST00000127403] [ENSMUST00000145082] [ENSMUST00000156474]
AlphaFold Q6P1G2
Predicted Effect probably damaging
Transcript: ENSMUST00000046073
AA Change: Y341N

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000038229
Gene: ENSMUSG00000029475
AA Change: Y341N

DomainStartEndE-ValueType
Blast:JmjC 23 101 4e-41 BLAST
JmjC 147 315 3.61e-41 SMART
low complexity region 380 401 N/A INTRINSIC
low complexity region 406 424 N/A INTRINSIC
PDB:2YU2|A 472 546 1e-17 PDB
Pfam:zf-CXXC 578 624 3e-17 PFAM
PHD 634 696 8.58e-4 SMART
low complexity region 792 823 N/A INTRINSIC
low complexity region 903 913 N/A INTRINSIC
low complexity region 990 1006 N/A INTRINSIC
low complexity region 1018 1032 N/A INTRINSIC
FBOX 1038 1078 1.69e-2 SMART
LRR 1121 1143 1.31e2 SMART
LRR 1145 1170 2.9e2 SMART
LRR 1185 1209 2.04e2 SMART
LRR 1210 1235 1.1e1 SMART
LRR 1265 1290 3.91e1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000086200
AA Change: Y335N

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000083376
Gene: ENSMUSG00000029475
AA Change: Y335N

DomainStartEndE-ValueType
Blast:JmjC 17 95 4e-41 BLAST
JmjC 141 309 3.61e-41 SMART
low complexity region 374 395 N/A INTRINSIC
low complexity region 400 418 N/A INTRINSIC
PDB:2YU2|A 466 540 1e-17 PDB
Pfam:zf-CXXC 572 618 2.1e-17 PFAM
PHD 628 690 8.58e-4 SMART
low complexity region 786 817 N/A INTRINSIC
low complexity region 897 907 N/A INTRINSIC
low complexity region 984 1000 N/A INTRINSIC
low complexity region 1012 1026 N/A INTRINSIC
FBOX 1032 1072 1.69e-2 SMART
LRR 1115 1137 1.31e2 SMART
LRR 1139 1164 2.9e2 SMART
LRR 1179 1203 2.04e2 SMART
LRR 1204 1229 1.1e1 SMART
LRR 1259 1284 3.91e1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000118027
AA Change: Y341N

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000114052
Gene: ENSMUSG00000029475
AA Change: Y341N

DomainStartEndE-ValueType
Blast:JmjC 23 101 4e-41 BLAST
JmjC 147 315 3.61e-41 SMART
low complexity region 380 401 N/A INTRINSIC
low complexity region 406 424 N/A INTRINSIC
PDB:2YU2|A 472 546 9e-18 PDB
Pfam:zf-CXXC 578 624 2.1e-17 PFAM
PHD 634 696 8.58e-4 SMART
low complexity region 865 875 N/A INTRINSIC
low complexity region 952 968 N/A INTRINSIC
low complexity region 980 994 N/A INTRINSIC
FBOX 1000 1040 1.69e-2 SMART
LRR 1083 1105 1.31e2 SMART
LRR 1107 1132 2.9e2 SMART
LRR 1147 1171 2.04e2 SMART
LRR 1172 1197 1.1e1 SMART
LRR 1227 1252 3.91e1 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000121739
AA Change: Y286N

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000114049
Gene: ENSMUSG00000029475
AA Change: Y286N

DomainStartEndE-ValueType
Blast:JmjC 1 46 2e-19 BLAST
JmjC 92 260 3.61e-41 SMART
low complexity region 325 346 N/A INTRINSIC
low complexity region 351 369 N/A INTRINSIC
PDB:2YU2|A 417 491 1e-17 PDB
Pfam:zf-CXXC 523 569 5.4e-17 PFAM
PHD 579 641 8.58e-4 SMART
low complexity region 737 768 N/A INTRINSIC
low complexity region 848 858 N/A INTRINSIC
low complexity region 935 951 N/A INTRINSIC
low complexity region 963 977 N/A INTRINSIC
FBOX 983 1023 1.69e-2 SMART
LRR 1066 1088 1.31e2 SMART
LRR 1090 1115 2.9e2 SMART
LRR 1130 1154 2.04e2 SMART
LRR 1155 1180 1.1e1 SMART
LRR 1210 1235 3.91e1 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000123479
Predicted Effect probably benign
Transcript: ENSMUST00000127403
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138929
Predicted Effect noncoding transcript
Transcript: ENSMUST00000143273
Predicted Effect probably damaging
Transcript: ENSMUST00000145082
AA Change: Y141N

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000114731
Gene: ENSMUSG00000029475
AA Change: Y141N

DomainStartEndE-ValueType
JmjC 1 115 4.87e-15 SMART
Blast:JmjC 118 286 7e-65 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000156474
AA Change: Y335N

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000118488
Gene: ENSMUSG00000029475
AA Change: Y335N

DomainStartEndE-ValueType
Blast:JmjC 17 95 3e-42 BLAST
JmjC 141 309 3.61e-41 SMART
low complexity region 374 395 N/A INTRINSIC
low complexity region 400 418 N/A INTRINSIC
PDB:2YU2|A 466 512 1e-8 PDB
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147544
Meta Mutation Damage Score 0.1101 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.3%
  • 20x: 97.8%
Validation Efficiency 98% (47/48)
MGI Phenotype FUNCTION: The protein encoded by this gene is a H3K36-specific histone demethylase, which contains an N-terminal jumonji C domain, a CxxC zinc finger domain, a plant homeodomain finger, an F-box, and eight leucine-rich repeats. Amongst its demonstrated functions, this protein plays roles in the suppression of premature cellular senescence, leukemia maintenance and development, maintenance of mouse embryonic stem cell pluripotency, and induced pluripotent stem cell generation. Mice homozygous for a targeted deletion of the zinc finger domain display embryonic lethality with development ceasing at approximately 7 to 8 days post coitum, demonstrating an essential role in early development. A pseudogene of this gene is found on chromosome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
PHENOTYPE: Mice homozygous for a targeted allele that does not express the long form protein exhibit exencephaly, fetal and postnatal lethality, coloboma, curly tail, oligozoospermia, increased apoptosis, and increased neuronal precursor proliferation. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Apol7b T A 15: 77,307,430 (GRCm39) Q355L probably benign Het
Asb14 A T 14: 26,633,945 (GRCm39) Q383H probably benign Het
Ash1l T G 3: 88,977,553 (GRCm39) M2661R probably damaging Het
Cacna1e G T 1: 154,577,313 (GRCm39) probably null Het
Ccdc40 G T 11: 119,150,870 (GRCm39) probably null Het
Cd27 T A 6: 125,210,188 (GRCm39) probably null Het
Ces3b T C 8: 105,817,385 (GRCm39) L371S possibly damaging Het
Clec4a2 T A 6: 123,117,711 (GRCm39) Y210N probably damaging Het
Cpeb2 A T 5: 43,394,681 (GRCm39) H553L Het
Cpne8 T C 15: 90,503,881 (GRCm39) I95V probably benign Het
D630039A03Rik T C 4: 57,910,525 (GRCm39) T96A probably benign Het
Dand5 C A 8: 85,543,147 (GRCm39) G110C probably damaging Het
Erich3 C T 3: 154,470,210 (GRCm39) T1554M unknown Het
Evi5l T C 8: 4,241,300 (GRCm39) S278P probably damaging Het
Farp2 C A 1: 93,548,325 (GRCm39) H1003Q probably damaging Het
G530012D18Rik C G 1: 85,504,935 (GRCm39) D113E unknown Het
Gm13741 A C 2: 87,486,446 (GRCm39) M273R possibly damaging Het
Gm28363 T A 1: 117,626,641 (GRCm39) D26E unknown Het
Gm8674 A T 13: 50,054,407 (GRCm39) D700E noncoding transcript Het
Gtf3c4 G A 2: 28,724,593 (GRCm39) Q380* probably null Het
Idh2 GGTCCCAG GG 7: 79,748,077 (GRCm39) probably benign Het
Il1a A T 2: 129,148,477 (GRCm39) S78T possibly damaging Het
Mcc T C 18: 44,582,508 (GRCm39) probably null Het
Met A G 6: 17,547,061 (GRCm39) D898G probably damaging Het
Mogs T C 6: 83,092,863 (GRCm39) V101A probably damaging Het
Mrgpra4 A T 7: 47,631,221 (GRCm39) Y127N probably damaging Het
Ms4a18 A G 19: 10,991,071 (GRCm39) S8P probably benign Het
Muc4 A T 16: 32,569,197 (GRCm39) T148S unknown Het
Nutm1 G A 2: 112,078,817 (GRCm39) L1033F probably benign Het
Ocstamp G T 2: 165,239,787 (GRCm39) A133D probably damaging Het
Or1ab2 T G 8: 72,864,253 (GRCm39) V281G noncoding transcript Het
Or5p63 T C 7: 107,810,995 (GRCm39) H247R probably damaging Het
Or8g17 T A 9: 38,930,249 (GRCm39) D196V probably benign Het
Or9s18 G A 13: 65,300,734 (GRCm39) R232Q probably damaging Het
Phf12 C A 11: 77,915,651 (GRCm39) P46Q probably damaging Het
Prf1 A G 10: 61,138,749 (GRCm39) T236A probably damaging Het
Ptcd3 A G 6: 71,884,798 (GRCm39) V47A probably benign Het
Rapgef1 A T 2: 29,626,011 (GRCm39) N1071Y probably damaging Het
Rftn1 G T 17: 50,354,408 (GRCm39) A318D probably damaging Het
Rnf26rt C A 6: 76,473,558 (GRCm39) A353S probably benign Het
Tango6 C T 8: 107,409,882 (GRCm39) P33L possibly damaging Het
Tasor2 G T 13: 3,649,691 (GRCm39) T36N probably damaging Het
Tbc1d2b C T 9: 90,089,937 (GRCm39) R864H probably damaging Het
Tent2 A G 13: 93,304,432 (GRCm39) probably null Het
Trav10n A T 14: 53,359,929 (GRCm39) I69L probably benign Het
Tsks A G 7: 44,603,296 (GRCm39) Q366R probably damaging Het
Vcan G T 13: 89,853,106 (GRCm39) S618* probably null Het
Vwf T A 6: 125,622,799 (GRCm39) probably null Het
Zfp827 T A 8: 79,787,206 (GRCm39) L124* probably null Het
Other mutations in Kdm2b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00578:Kdm2b APN 5 123,099,630 (GRCm39) missense probably damaging 1.00
IGL02061:Kdm2b APN 5 123,021,404 (GRCm39) missense probably damaging 1.00
IGL02142:Kdm2b APN 5 123,085,898 (GRCm39) missense probably damaging 0.99
IGL02143:Kdm2b APN 5 123,085,898 (GRCm39) missense probably damaging 0.99
IGL02147:Kdm2b APN 5 123,085,898 (GRCm39) missense probably damaging 0.99
IGL02294:Kdm2b APN 5 123,099,537 (GRCm39) missense probably damaging 1.00
IGL02309:Kdm2b APN 5 123,085,883 (GRCm39) missense probably damaging 0.99
IGL03039:Kdm2b APN 5 123,019,734 (GRCm39) missense probably benign 0.06
IGL03134:Kdm2b UTSW 5 123,070,737 (GRCm39) missense probably damaging 1.00
PIT4520001:Kdm2b UTSW 5 123,079,110 (GRCm39) missense probably damaging 1.00
R0008:Kdm2b UTSW 5 123,019,806 (GRCm39) missense probably benign 0.08
R0592:Kdm2b UTSW 5 123,099,197 (GRCm39) splice site probably benign
R0894:Kdm2b UTSW 5 123,122,523 (GRCm39) critical splice donor site probably null
R1078:Kdm2b UTSW 5 123,099,604 (GRCm39) missense possibly damaging 0.83
R1387:Kdm2b UTSW 5 123,018,331 (GRCm39) missense probably damaging 1.00
R1441:Kdm2b UTSW 5 123,070,943 (GRCm39) missense probably benign 0.25
R1550:Kdm2b UTSW 5 123,019,120 (GRCm39) missense probably damaging 1.00
R1795:Kdm2b UTSW 5 123,122,523 (GRCm39) critical splice donor site probably null
R2060:Kdm2b UTSW 5 123,021,428 (GRCm39) missense probably damaging 1.00
R2161:Kdm2b UTSW 5 123,018,762 (GRCm39) missense probably damaging 1.00
R2259:Kdm2b UTSW 5 123,020,479 (GRCm39) missense probably damaging 1.00
R3843:Kdm2b UTSW 5 123,072,856 (GRCm39) missense probably damaging 0.98
R3844:Kdm2b UTSW 5 123,072,856 (GRCm39) missense probably damaging 0.98
R3859:Kdm2b UTSW 5 123,018,290 (GRCm39) missense probably damaging 1.00
R4506:Kdm2b UTSW 5 123,026,688 (GRCm39) missense possibly damaging 0.58
R4680:Kdm2b UTSW 5 123,072,849 (GRCm39) missense probably damaging 0.99
R4786:Kdm2b UTSW 5 123,018,917 (GRCm39) critical splice acceptor site probably null
R4894:Kdm2b UTSW 5 123,079,030 (GRCm39) nonsense probably null
R5265:Kdm2b UTSW 5 123,016,651 (GRCm39) missense probably damaging 1.00
R5522:Kdm2b UTSW 5 123,087,225 (GRCm39) missense probably damaging 1.00
R5746:Kdm2b UTSW 5 123,017,427 (GRCm39) missense probably damaging 1.00
R5813:Kdm2b UTSW 5 123,009,931 (GRCm39) missense probably benign 0.37
R5920:Kdm2b UTSW 5 123,018,359 (GRCm39) missense probably damaging 1.00
R5961:Kdm2b UTSW 5 123,070,724 (GRCm39) missense probably benign 0.37
R6029:Kdm2b UTSW 5 123,017,650 (GRCm39) missense probably damaging 1.00
R6280:Kdm2b UTSW 5 123,016,687 (GRCm39) missense probably damaging 1.00
R6303:Kdm2b UTSW 5 123,019,807 (GRCm39) missense probably benign 0.34
R6304:Kdm2b UTSW 5 123,019,807 (GRCm39) missense probably benign 0.34
R6383:Kdm2b UTSW 5 123,072,841 (GRCm39) missense probably damaging 1.00
R6432:Kdm2b UTSW 5 123,018,254 (GRCm39) missense probably damaging 1.00
R6513:Kdm2b UTSW 5 123,018,302 (GRCm39) missense probably damaging 0.99
R6526:Kdm2b UTSW 5 123,099,532 (GRCm39) missense probably damaging 1.00
R7213:Kdm2b UTSW 5 123,059,532 (GRCm39) missense probably damaging 0.99
R7226:Kdm2b UTSW 5 123,059,512 (GRCm39) missense possibly damaging 0.60
R7292:Kdm2b UTSW 5 123,018,854 (GRCm39) missense probably damaging 0.98
R7893:Kdm2b UTSW 5 123,085,802 (GRCm39) missense probably benign 0.12
R8021:Kdm2b UTSW 5 123,070,982 (GRCm39) missense probably damaging 0.99
R8038:Kdm2b UTSW 5 123,098,958 (GRCm39) intron probably benign
R8397:Kdm2b UTSW 5 123,018,579 (GRCm39) missense probably benign 0.03
R8411:Kdm2b UTSW 5 123,018,239 (GRCm39) missense probably damaging 1.00
R8899:Kdm2b UTSW 5 123,125,851 (GRCm39) nonsense probably null
R8997:Kdm2b UTSW 5 123,018,236 (GRCm39) missense probably null 0.99
R9142:Kdm2b UTSW 5 123,127,112 (GRCm39) unclassified probably benign
R9192:Kdm2b UTSW 5 123,070,679 (GRCm39) missense probably benign 0.05
R9238:Kdm2b UTSW 5 123,009,889 (GRCm39) missense probably damaging 0.98
R9455:Kdm2b UTSW 5 123,099,537 (GRCm39) missense probably damaging 1.00
R9644:Kdm2b UTSW 5 123,120,842 (GRCm39) missense probably damaging 0.98
R9731:Kdm2b UTSW 5 123,125,823 (GRCm39) missense probably benign 0.03
Z1177:Kdm2b UTSW 5 123,018,860 (GRCm39) missense probably damaging 0.98
Predicted Primers PCR Primer
(F):5'- TCTAGGTTGGAGGCTCACAAG -3'
(R):5'- TCACAAAGATGGGTGAGCTC -3'

Sequencing Primer
(F):5'- ATTTCCTGAGAGGCCTAATGTCCAG -3'
(R):5'- TCACAAAGATGGGTGAGCTCTTATAG -3'
Posted On 2020-07-13